Afghan President Hamid Karzai, left, talks with U.N. Secretary-General Ban Ki Moon at the presidential palace in Kabul on Monday.

By Jim Michaels, USA TODAY

KABUL  Afghan President Hamid Karzai formally won a second five-year term Monday, but his opponent expressed concerns about the contentious election.

Afghanistan's Independent Election Commission declared Karzai the winner and canceled Saturday's runoff, one day after Abdullah Abdullah withdrew from the race, saying the system was corrupt.

President Obama said he spoke to Karzai to congratulate him on his victory and to call for a "new chapter" of better governance after the fraud-ridden election. Obama called the election process "messy" but said Karzai won in accordance with Afghan law.

"I emphasized that this has to be a point in time in which we begin to write a new chapter," Obama said in describing his phone call to the Afghan president. Obama said that when Karzai offered his assurances, Obama told him, "The proof is not going to be in words. It's going to be in deeds."

The White House has been waiting for a legitimate government to be in place before deciding whether to send more U.S. troops to fight a growing insurgency in Afghanistan.

Britain and the United Nations issued statements congratulating Karzai.

Afghanistan's government has been in political uncertainty since the election Aug. 20, which was marred by widespread fraud that inflated votes for Karzai.

The election commission ordered a runoff between Karzai and Abdullah, the top vote getters, after fraud investigators threw out nearly a third of Karzai's votes, dropping him below the 50% threshold needed to win outright.

As the political standoff grew more intense in recent weeks, Abdullah insisted on changes to the election commission, saying it is biased because the members are appointed by Karzai. Abdullah announced Sunday that he was dropping out of the runoff because the voting would be rigged against him.

In an interview Monday at his villa in Kabul, Abdullah said he would continue to promote the principles that he raised in his campaign for a stronger rule of law and more transparency in Afghanistan's government.

"This atmosphere of uncertainty here is not helpful at all," Abdullah said about the questions surrounding the election process.

Abdullah, a former foreign minister, appeared tired and his voice sounded weak during the interview, conducted before the election commission made its formal announcement.

Abdullah said he had met with Karzai a few days before withdrawing from the runoff and had narrowed his demands to a single request: the removal of the election commission chairman.

"I reduced those conditions to one single one," Abdullah said. "He refused."

A Karzai spokesman could not be reached for comment.

Abdullah suggested he might create a national party but said he no such immediate plans. "There aren't many nationally based political parties," he said. "This is one of the shortcomings in this system."

A spokesman said later that Abdullah would give a speech today with his reaction.

"We expected that this commission would announce something like this, because this commission has never been independent and has always supported President Karzai," Fazel Sancharaki said.

Election commission Chairman Azizullah Lodin said the commission had the authority to make its decision because the Afghan constitution allows for a runoff only between two candidates.

White House spokesman Robert Gibbs said, "Now begin the hard conversations about ensuring credibility, ensuring and improving governance, addressing corruption. We are focused on what has to happen in order to have a credible partner."

U.N. Secretary-General Ban Ki Moon, who was in Kabul on a surprise visit, welcomed the decision to forgo the runoff.

"This has been a difficult election process for Afghanistan, and lessons must be learned," he said. "Afghanistan now faces significant challenges, and the new president must move swiftly to form a government that is able to command the support of both the Afghan people and the international community."

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